How do I composite a transparent texture over a masked Render Layer
Your "skydome" renderlayer is masked, and it shouldn't.

Remove the mask from the background renderlayer and the alpha over operation will produce the right result.

The skydome renderlayer should look fully opaque, without any transparency (your screenshot shows that it is masked by the objects of the foreground renderlayer).

Keep in mind that masks in the renderlayer panel are z-masks, created by geometry, and not affected by alpha transparency.